I was wondering the same thing, as I was intending on using Dual Wielding and I have a player who took Rapid Fire. I think I'm ruling that it does. But I'm trying to figure out how target switching with multiple handgun shots actually works. Right now my thought is:
1) The talent only applies to the main hand gun, second gun shots will still take a penalty die. So up to three shots without penalty die, and then up to 3 more with (I still have some confusion around number of targets...)
2) They can fire at a single target with both, and don't take a penalty die an any of the shots at a single target
3) Same as (2) but they can choose two targets, but take a penalty die on the second target (they are essentially focusing on shooting at one target)
4) They can fire at two targets (one with each gun) and don't take a penalty die
5) They can fire at any number of targets, with no penalty die
Honestly it's not totally clear to me how the handgun multiple fire is supposed to work for if they can choose multiple targets or not. At the moment I think I'm leaning towards (1) or (2).